def test_scramble_identity():
mill = qcel.molutil.compute_scramble(4,
do_resort=False,
do_shift=False,
do_rotate=False,
deflection=1.0,
do_mirror=False)
mill_str = """----------------------------------------
AlignmentMill
eye
----------------------------------------
Mirror: False
Atom Map: [0 1 2 3]
Shift: [0. 0. 0.]
Rotation:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
----------------------------------------"""
assert compare(mill_str, mill.pretty_print(label="eye"))
mill_dict = {
"shift": [0.0, 0.0, 0.0],
"rotation": [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
"atommap": [0, 1, 2, 3],
"mirror": False,
}
assert compare_recursive(mill_dict, mill.dict())
mill_dict["rotation"] = [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0]
assert compare_recursive(mill_dict, mill.dict(encoding="json"))
def test_scramble_identity():
mill = qcel.molutil.compute_scramble(4,
do_resort=False,
do_shift=False,
do_rotate=False,
deflection=1.0,
do_mirror=False)
mill_str = """----------------------------------------
AlignmentMill
eye
----------------------------------------
Mirror: False
Atom Map: [0 1 2 3]
Shift: [0. 0. 0.]
Rotation:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
----------------------------------------"""
assert compare(mill_str, mill.__str__(label='eye'))
mill_dict = {
'shift': [0., 0., 0.],
'rotation': [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]],
'atommap': [0, 1, 2, 3],
'mirror': False
}
assert compare_recursive(mill_dict, mill.dict())
mill_dict['rotation'] = [1., 0., 0., 0., 1., 0., 0., 0., 1.]
assert compare_recursive(mill_dict, mill.dict(encoding="json"))
def test_dftd3__from_arrays(inp, expected):
res = empirical_dispersion_resources.from_arrays(**inp[0])
assert compare_recursive(expected, res, atol=1.e-4)
assert compare(inp[1], _compute_key(res), 'key')
res = empirical_dispersion_resources.from_arrays(name_hint=res['fctldash'],
level_hint=res['dashlevel'],
param_tweaks=res['dashparams'])
assert compare_recursive(expected, res, tnm() + ' idempotent', atol=1.e-4)
def test_b1_computeBE(b1_water):
EnergyThre = 1e-6
BE_blyp = b1_water.computeBE("blyp")
expected = 0.33100268529368293
assert compare_recursive(BE_blyp, expected, atol=EnergyThre)
BE_b1lyp = b1_water.computeBE("b1lyp")
expected = 0.3183329645632256
assert compare_recursive(BE_b1lyp, expected, atol=EnergyThre)
def test_formula_to_elements():
assert compare_recursive(formula_to_elements("C2H6O"), {
"C": 2,
"H": 6,
"O": 1
})
assert compare_recursive(formula_to_elements("C2H6OOO"), {
"C": 2,
"H": 6,
"O": 3
})
def test_diagnostic_factory_B1(qcelemental_water):
calculator = MultirefPredict.diagnostic_factory("B1",
molecule=qcelemental_water)
diag = calculator.computeDiagnostic()
B1Thre = 1e-6
expected = 0.006334860365228678
assert compare_recursive(diag, expected, atol=B1Thre)
def test_diagnostic_factory_A25PBE(qcelemental_water):
calculator = MultirefPredict.diagnostic_factory("A25PBE",
molecule=qcelemental_water)
diag = calculator.computeDiagnostic()
A25PBEThre = 1e-6
expected = 0.1626572016077259
assert compare_recursive(diag, expected, atol=A25PBEThre)
def test_diagnostic_factory_TAE(qcelemental_water):
calculator = MultirefPredict.diagnostic_factory("TAE",
molecule=qcelemental_water)
diag = calculator.computeDiagnostic()
TAEThre = 1e-6
expected = 0.28078682517214126
assert compare_recursive(diag, expected, atol=TAEThre)
def test_qchem_logfile_parser(test_case):
# Get output file data
data = qchem_logonly_info.get_test_data(test_case)
outfiles = {"dispatch.out": data["qchem.out"]}
with pytest.warns(Warning):
output = qcng.get_program("qchem",
check=False).parse_logfile(outfiles).dict()
output["stdout"] = None
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
for key in list(output["provenance"].keys()):
if key not in output_ref["provenance"]:
output["provenance"].pop(key)
# Modify ref to trim down total data as a molecule is now sparse
output_ref["molecule"] = {
k: v
for k, v in output_ref["molecule"].items() if k in output["molecule"]
}
check, message = compare_recursive(output_ref,
output,
return_message=True,
forgive=qchem_forgive)
assert check, message
def test_qchem_logfile_parser_qcscr(test_case):
# Get output file data
data = qchem_info.get_test_data(test_case)
outfiles = qcel.util.deserialize(data["outfiles.msgpack"], "msgpack-ext")
with pytest.warns(Warning):
output = qcng.get_program("qchem",
check=False).parse_logfile(outfiles).dict()
output["stdout"] = None
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
for key in list(output["provenance"].keys()):
if key not in output_ref["provenance"]:
output["provenance"].pop(key)
output_ref["stdout"] = None
# Modify ref to trim down total data as a molecule is now sparse
output_ref["molecule"] = {
k: v
for k, v in output_ref["molecule"].items() if k in output["molecule"]
}
output_ref["model"]["method"] = output_ref["model"]["method"].lower()
check, message = compare_recursive(output_ref,
output,
return_message=True,
forgive=qchem_forgive)
assert check, message
def test_fon_task(fon_trityl_radical, trityl_radical_task):
with pytest.raises(ValueError):
fon_task = fon_trityl_radical.FonTask(fon_trityl_radical.molecule, "psi4", "PBE")
fon_task = fon_trityl_radical.FonTask(fon_trityl_radical.molecule,"terachem","PBE")
Thre = 1e-6
assert compare_recursive(fon_task.dict()['keywords'], trityl_radical_task.dict()['keywords'], atol=Thre)
def test_qchem_logfile_parser_qcscr(test_case):
# Get output file data
data = qchem_info.get_test_data(test_case)
outfiles = qcel.util.deserialize(data["outfiles.msgpack"], "msgpack-ext")
with pytest.warns(Warning):
output = qcng.get_program("qchem",
check=False).parse_logfile(outfiles).dict()
output["stdout"] = None
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
for key in list(output["provenance"].keys()):
if key not in output_ref["provenance"]:
output["provenance"].pop(key)
output_ref["stdout"] = None
# compare_recursive.forgive can be used once QCEL#174 is released
output["molecule"].pop("connectivity")
output_ref["molecule"].pop("connectivity")
output_ref["model"]["method"] = output_ref["model"]["method"].lower()
check, message = compare_recursive(
output_ref,
output,
return_message=True,
forgive=[
"root.molecule.provenance.version", "root.provenance.version",
"root.provenance.routine"
],
)
assert check, message
def test_fon_computeDiagnostic(fon_cu_complex):
Thre = 1e-2
diag = fon_cu_complex.computeDiagnostic()
expected = {'FOD': 0.980722,
'Mattito':{ 'I_D': 0.473731315028, 'I_ND': 0.431365088635},
'Entanglement': 0.732773215873}
print(diag)
assert compare_recursive(diag, expected, atol=Thre)
def test_fon_b3lyp(fon_trityl_radical):
Thre = 1e-2
diag2 = fon_trityl_radical.computeDiagnostic("b3lyp")
expected2 = {'FOD': 0.7340689999999996,
'Mattito': {'I_D': 0.7479020997602953, 'I_ND': 0.33741997473349994},
'Entanglement': -1}
print(diag2)
assert compare_recursive(diag2, expected2, atol=Thre)
def test_fon_unrestricted(fon_trityl_radical):
Thre = 1e-2
diag = fon_trityl_radical.computeDiagnostic()
expected = {'FOD': 0.34399500000000005,
'Mattito': {'I_D': 0.39268800205639215, 'I_ND': 0.16333423895850002},
'Entanglement': -1}
print(diag)
assert compare_recursive(diag, expected, atol=Thre)
def test_terachem_output_parser(test_case):
# Get output file data
data = terachem_info.get_test_data(test_case)
inp = qcel.models.ResultInput.parse_raw(data["input.json"])
output = qcng.get_program('terachem', check=False).parse_output(data, inp)
output_ref = qcel.models.Result.parse_raw(data["output.json"])
assert compare_recursive(output_ref.dict(), output.dict())
def test_terachem_output_parser(test_case):
# Get output file data
data = terachem_info.get_test_data(test_case)
inp = qcel.models.AtomicInput.parse_raw(data["input.json"])
output = qcng.get_program("terachem", check=False).parse_output(data, inp).dict()
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
# Forgiving molecule since it is now sparse
assert compare_recursive(output_ref, output, forgive={"stdout", "provenance", "molecule"})
def test_complex_array():
datum1 = qcel.Datum('complex array', '', np.arange(3, dtype=np.complex_) + 1j)
ans = {
'label': 'complex array',
'units': '',
'data': [complex(0, 1), complex(1, 1), complex(2, 1)],
'numeric': True
}
dicary = datum1.dict()
assert compare_recursive(ans, dicary, 9)
def test_cc_computeDiagnostic(cc_water):
Thre = 1e-6
diag = cc_water.computeDiagnostic()
expected = {
'T1': 0.005903453140867589,
'D1': 0.012965638464472996,
'D2': 0.12885433260716933,
'New D1': 0.012965638464472996
}
print(diag)
assert compare_recursive(diag, expected, atol=Thre)
def test_to_dict(dataset):
listans = [i * 4 / 3 for i in range(4)]
ans = {
'label': 'an array',
'units': 'cm^-1',
'data': listans,
'comment': 'freqs'
}
dicary = dataset['ndarray'].dict()
assert compare_recursive(ans, dicary, 9)
def test_complex_scalar():
datum1 = qcel.Datum('complex scalar', '', complex(1, 2))
ans = {'label': 'complex scalar', 'units': '', 'data': complex(1, 2)}
assert datum1.label == 'complex scalar'
assert datum1.units == ''
assert datum1.data.real == 1
assert datum1.data.imag == 2
dicary = datum1.dict()
assert compare_recursive(ans, dicary, 9)
def test_complex_array():
datum1 = qcel.Datum('complex array', '',
np.arange(3, dtype=np.complex_) + 1j)
ans = {
'label': 'complex array',
'units': '',
'data': [[0.0, 1.0, 2.0], [1.0, 1.0, 1.0]]
}
dicary = datum1.to_dict()
assert compare_recursive(ans, dicary, 9)
def test_to_dict(dataset):
listans = [i * 4 / 3 for i in range(4)]
ans = {
"label": "an array",
"units": "cm^-1",
"data": listans,
"comment": "freqs",
"numeric": True
}
dicary = dataset["ndarray"].dict()
assert compare_recursive(ans, dicary, 9)
def test_dftd3__from_arrays__supplement():
ans = {
'dashlevel': 'chg',
'dashparams': {
's6': 4.05
},
'fctldash': 'asdf-d4',
'dashparams_citation': ' mypaper\n'
}
supp = {'chg': {'definitions': {'asdf-d4': {'params': {'s6': 4.05}, 'citation': ' mypaper\n'}}}}
res = dftd3.from_arrays(name_hint='asdf-d4', level_hint='chg', dashcoeff_supplement=supp)
assert compare_recursive(ans, res, atol=1.e-4)
with pytest.raises(ValueError) as e:
dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
assert "Can't guess -D correction level" in str(e)
res = dftd3.from_arrays(
name_hint=res['fctldash'],
level_hint=res['dashlevel'],
param_tweaks=res['dashparams'],
dashcoeff_supplement=supp)
assert compare_recursive(ans, res, tnm() + ' idempotent', atol=1.e-4)
def test_diagnostic_factory_D2(qcelemental_water):
Thre = 1e-6
calculator = MultirefPredict.diagnostic_factory("D2",
molecule=qcelemental_water)
diag = calculator.computeDiagnostic()
expected = {
'T1': 0.005903453140867589,
'D1': 0.012965638464472996,
'D2': 0.12885433260716933,
'New D1': 0.012965638464472996
}
print(diag)
assert compare_recursive(diag, expected, atol=Thre)
def test_complex_array():
datum1 = qcel.Datum("complex array", "",
np.arange(3, dtype=np.complex_) + 1j)
ans = {
"label": "complex array",
"units": "",
"data": [complex(0, 1), complex(1, 1),
complex(2, 1)],
"numeric": True,
}
dicary = datum1.dict()
assert compare_recursive(ans, dicary, 9)
def test_dftd3__from_arrays__supplement():
ans = {
'dashlevel': 'chg',
'dashparams': {
's6': 4.05
},
'fctldash': 'asdf-d4',
'dashparams_citation': ' mypaper\n'
}
supp = {'chg': {'definitions': {'asdf-d4': {'params': {'s6': 4.05}, 'citation': ' mypaper\n'}}}}
res = dftd3.from_arrays(name_hint='asdf-d4', level_hint='chg', dashcoeff_supplement=supp)
assert compare_recursive(ans, res, atol=1.e-4)
with pytest.raises(ValueError) as e:
dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
assert "Can't guess -D correction level" in str(e)
res = dftd3.from_arrays(
name_hint=res['fctldash'],
level_hint=res['dashlevel'],
param_tweaks=res['dashparams'],
dashcoeff_supplement=supp)
assert compare_recursive(ans, res, tnm() + ' idempotent', atol=1.e-4)
def test_entos_output_parser(test_case):
# Get output file data
data = entos_info.get_test_data(test_case)
inp = qcel.models.AtomicInput.parse_raw(data["input.json"])
output = qcng.get_program("entos", check=False).parse_output(data, inp).dict()
output.pop("provenance", None)
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
output_ref.pop("provenance", None)
check = compare_recursive(output_ref, output)
assert check, (output, output_ref)
def test_qchem_executor(test_case):
# Get input file data
data = qchem_info.get_test_data(test_case)
inp = qcel.models.AtomicInput.parse_raw(data["input.json"])
# Run qchem
result = qcng.compute(inp, "qchem")
assert result.success is True
# Get output file data
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"])
atol = 1e-6
assert compare_recursive(output_ref.return_result, result.return_result, atol=atol)
def test_qchem_output_parser(test_case):
# Get output file data
data = qchem_info.get_test_data(test_case)
inp = qcel.models.AtomicInput.parse_raw(data["input.json"])
outfiles = qcel.util.deserialize(data["outfiles.msgpack"], "msgpack-ext")
output = qcng.get_program("qchem", check=False).parse_output(outfiles, inp).dict()
output.pop("provenance", None)
output_ref = qcel.models.AtomicResult.parse_raw(data["output.json"]).dict()
output_ref.pop("provenance", None)
check, message = compare_recursive(output_ref, output, return_message=True)
assert check, message
def test_molpro_output_parser(test_case):
# Get output file data
data = molpro_info.get_test_data(test_case)
inp = qcel.models.ResultInput.parse_raw(data["input.json"])
output = qcng.get_program('molpro').parse_output(data, inp).dict()
output.pop("provenance", None)
output_ref = qcel.models.Result.parse_raw(data["output.json"]).dict()
output_ref.pop("provenance", None)
# TODO add `skip` to compare_recusive
check = compare_recursive(output_ref, output)
assert check, check
def test_dftd3__from_arrays(inp, expected):
res = dftd3.from_arrays(**inp[0])
assert compare_recursive(expected, res, atol=1.e-4)
assert compare(inp[1], _compute_key(res), 'key')
res = dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
assert compare_recursive(expected, res, tnm() + ' idempotent', atol=1.e-4)